The effects of substrate surface loading rate on biofilm growth and structure were investigated by chemical, biochemical and microscopic methods. Three tubular reactors were operated at equal C:N ratio of 0.1, with substrate loading rates of 1.2, 0.6 and 0.3 g-C/m 2/day. Substrate loading positively influenced the biofilm growth rate. Denser biofilms with lower porosities were formed at higher substrate loading. Slowly growing biofilms having porous structures were found to have higher specific activities. Nitrification was suppressed under the higher substrate loading conditions even at the equal C:N ratio of 0.1, thus proving that the spatial competition between nitrifiers and heterotrophs as one limiting criteria for stable nitrification. The spatial organization of the ammonia oxidizers was biofilm structure related. The strain variability of ammonia oxidizers was substrate loading dependent. These findings suggest that substrate loading is a key parameter in determining biofilm structure and function.